Turkish Airlines has issued an announcement about how they are handling this.
https://p.turkishairlines.com/en-us/...ase/index.html
Dear Passengers,
Due to the recent developments some changes have been made on Turkey-USA and USA-Turkey visa application processes. These changes do not affect passengers transferring to connecting flights in Istanbul.
Excluding passengers transferring to connecting flights in Istanbul; for all passengers holding Turkish passports flying to the USA and all passengers holding American passports flying to Turkey on Turkish Airlines and AnadoluJet Turkey-USA and USA-Turkey flights between October 9th, 2017 and October 31st, 2017, with tickets issued on or before October 9th, 2017, the following procedure can be carried out till October 31st, 2017:
See link for further details.